Input image strip without stretching to fit output frame
The default behaviour of an image strip added to the VSE is to scale to the render resolution set for the blend file. To change this behaviour in the way you have specified; enable "Image Offset" in the Strip Input panel on the properties bar for the selected image sequence, then use the X and Y value inputs to position the image within the output image space. You also want to set the blend type to "Alpha Over" so that the underlying strip is visible.